If more than 50 genes/sequences are provided as input, then the associated running time can take some time. Therefore it is advisable to provide an email-address in case you are running the Interactive Phylogenetics Module with more than 50 genes. After processing you will be send an email with a link to the created phylogenetic tree.
The selection modi are exclusive: please choose either Gene selection or Species selection.
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ) $local_species = 'acertr' $disabled = '' $selected = ''include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0;
$disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":"";
$selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":"";
$num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0;
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ) $local_species = 'acertr' $disabled = '' $selected = ''
include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ) $local_species = 'ach' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ) $local_species = 'ach' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ) $local_species = 'aar' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ) $local_species = 'aar' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ) $local_species = 'amhyb' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ) $local_species = 'amhyb' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ) $local_species = 'atr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ) $local_species = 'atr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ) $local_species = 'aag' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ) $local_species = 'aag' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ) $local_species = 'aly' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ) $local_species = 'aly' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ) $local_species = 'ath' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ) $local_species = 'ath' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ) $local_species = 'arhy' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ) $local_species = 'arhy' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ) $local_species = 'ama' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ) $local_species = 'ama' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ) $local_species = 'bvu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ) $local_species = 'bvu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ) $local_species = 'bca' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ) $local_species = 'bca' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ) $local_species = 'bna' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ) $local_species = 'bna' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ) $local_species = 'bol' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ) $local_species = 'bol' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ) $local_species = 'bra' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ) $local_species = 'bra' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ) $local_species = 'camsi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ) $local_species = 'camsi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ) $local_species = 'cansat' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ) $local_species = 'cansat' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ) $local_species = 'cru' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ) $local_species = 'cru' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ) $local_species = 'can' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ) $local_species = 'can' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ) $local_species = 'chi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ) $local_species = 'chi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ) $local_species = 'cpa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ) $local_species = 'cpa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ) $local_species = 'cfa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ) $local_species = 'cfa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ) $local_species = 'cil' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ) $local_species = 'cil' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ) $local_species = 'cde' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ) $local_species = 'cde' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ) $local_species = 'cla' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ) $local_species = 'cla' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ) $local_species = 'ccl' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ) $local_species = 'ccl' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ) $local_species = 'ccan' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ) $local_species = 'ccan' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ) $local_species = 'col' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ) $local_species = 'col' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ) $local_species = 'cav' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ) $local_species = 'cav' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ) $local_species = 'cme' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ) $local_species = 'cme' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ) $local_species = 'csa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ) $local_species = 'csa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ) $local_species = 'dca' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ) $local_species = 'dca' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ) $local_species = 'din' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ) $local_species = 'din' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ) $local_species = 'dzi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ) $local_species = 'dzi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ) $local_species = 'eca' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ) $local_species = 'eca' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ) $local_species = 'egut' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ) $local_species = 'egut' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ) $local_species = 'egr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ) $local_species = 'egr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ) $local_species = 'esa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ) $local_species = 'esa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ) $local_species = 'fve' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ) $local_species = 'fve' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ) $local_species = 'fan' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ) $local_species = 'fan' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ) $local_species = 'gma' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ) $local_species = 'gma' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ) $local_species = 'ghi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ) $local_species = 'ghi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ) $local_species = 'gra' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ) $local_species = 'gra' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ) $local_species = 'han' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ) $local_species = 'han' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ) $local_species = 'hma' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ) $local_species = 'hma' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ) $local_species = 'lsa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ) $local_species = 'lsa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ) $local_species = 'lonja' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ) $local_species = 'lonja' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ) $local_species = 'lja' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ) $local_species = 'lja' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ) $local_species = 'lal' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ) $local_species = 'lal' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ) $local_species = 'mbi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ) $local_species = 'mbi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ) $local_species = 'mdo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ) $local_species = 'mdo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ) $local_species = 'mes' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ) $local_species = 'mes' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ) $local_species = 'mpo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ) $local_species = 'mpo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ) $local_species = 'nta' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ) $local_species = 'nta' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ) $local_species = 'oeu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ) $local_species = 'oeu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ) $local_species = 'osa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ) $local_species = 'osa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ) $local_species = 'pso' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ) $local_species = 'pso' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ) $local_species = 'pax' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ) $local_species = 'pax' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ) $local_species = 'pvu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ) $local_species = 'pvu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ) $local_species = 'ppa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ) $local_species = 'ppa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ) $local_species = 'ptr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ) $local_species = 'ptr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ) $local_species = 'pgr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ) $local_species = 'pgr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ) $local_species = 'qlo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ) $local_species = 'qlo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ) $local_species = 'rsi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ) $local_species = 'rsi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ) $local_species = 'rch' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ) $local_species = 'rch' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ) $local_species = 'sbr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ) $local_species = 'sbr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ) $local_species = 'sbo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ) $local_species = 'sbo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ) $local_species = 'sed' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ) $local_species = 'sed' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ) $local_species = 'smo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ) $local_species = 'smo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ) $local_species = 'sci' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ) $local_species = 'sci' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ) $local_species = 'sly' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ) $local_species = 'sly' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ) $local_species = 'spe' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ) $local_species = 'spe' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ) $local_species = 'stu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ) $local_species = 'stu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ) $local_species = 'sas' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ) $local_species = 'sas' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ) $local_species = 'tha' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ) $local_species = 'tha' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ) $local_species = 'tca' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ) $local_species = 'tca' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ) $local_species = 'tpr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ) $local_species = 'tpr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ) $local_species = 'twi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ) $local_species = 'twi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ) $local_species = 'tar' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ) $local_species = 'tar' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ) $local_species = 'ugi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ) $local_species = 'ugi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ) $local_species = 'vma' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ) $local_species = 'vma' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ) $local_species = 'vpl' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ) $local_species = 'vpl' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ) $local_species = 'vmu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ) $local_species = 'vmu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ) $local_species = 'vvi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ) $local_species = 'vvi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) $local_species = 'zma' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ), 'gf_id' => 'HOM05D001177', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001177' ), 'data_identifier' => 'HOM05D001177', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001177', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01600' => 'bna', 'A02p35380' => 'bna', 'A02p35390' => 'bna', 'A06p41270' => 'bna', 'A07p20470' => 'bna', 'A07p20480' => 'bna', 'A08p27820' => 'bna', 'A09p40620' => 'bna', 'Aa31LG2G5370' => 'aar', 'Aa31LG6G2570' => 'aar', 'Aa31LG7G7990' => 'aar', 'Aa31LG9G920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1330' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1782' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5695' => 'aag', 'Actinidia08195' => 'ach', 'Actinidia15502' => 'ach', 'Actinidia17052' => 'ach', 'Actinidia24654' => 'ach', 'Actinidia36158' => 'ach', 'Actinidia36159' => 'ach', 'Ah.02g130620' => 'amhyb', 'Ah.02g131670' => 'amhyb', 'Ah.03g132110' => 'amhyb', 'Ah.11g041610' => 'amhyb', 'AL1G38250' => 'aly', 'AL5G16650' => 'aly', 'AL7G13400' => 'aly', 'AL7G49020' => 'aly', 'Aqoxy3G00857' => 'aox', 'Aqoxy3G01086' => 'aox', 'Aqoxy3G03166' => 'aox', 'Aqoxy5G01019' => 'aox', 'Aqoxy5G03563' => 'aox', 'Aqoxy5G03571' => 'aox', 'Aqoxy6G01632' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1S388T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.50T0BQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q0SVNI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R689L2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W74W8S' => 'arhy', 'AT1G27200' => 'ath', 'AT3G27330' => 'ath', 'AT4G37420' => 'ath', 'AT5G40720' => 'ath', 'ATR0712G160' => 'atr', 'ATR0807G028' => 'atr', 'ATR0824G069' => 'atr', 'ATR0824G077' => 'atr', 'Atru.chr11.1923' => 'acertr', 'Atru.chr13.125' => 'acertr', 'Atru.chr6.2478' => 'acertr', 'Atru.chr6.2479' => 'acertr', 'AUR62005578' => 'cqu', 'AUR62024152' => 'cqu', 'AUR62026531' => 'cqu', 'AUR62035128' => 'cqu', 'AUR62039450' => 'cqu', 'BcaB02g07931' => 'bca', 'BcaB03g11972' => 'bca', 'BcaB07g32396' => 'bca', 'BcaC03g14536' => 'bca', 'BcaC05g26335' => 'bca', 'BcaC06g31011' => 'bca', 'BcaC06g33828' => 'bca', 'BcaC07g39241' => 'bca', 'BcaC08g44478' => 'bca', 'BcaNung04756' => 'bca', 'BolC1t00166H' => 'bol', 'BolC2t11472H' => 'bol', 'BolC5t31056H' => 'bol', 'BolC6t37128H' => 'bol', 'BolC7t44157H' => 'bol', 'BolC8t49880H' => 'bol', 'BraA01t00151Z' => 'bra', 'BraA02t08540Z' => 'bra', 'BraA06t27051Z' => 'bra', 'BraA07t29741Z' => 'bra', 'BraA08t34714Z' => 'bra', 'BraA09t39558Z' => 'bra', 'C01p01720' => 'bna', 'C02p54100' => 'bna', 'C05p23440' => 'bna', 'C06p19330' => 'bna', 'C07p36380' => 'bna', 'C07p39030' => 'bna', 'C08p22460' => 'bna', 'C08p35970' => 'bna', 'C09p60530' => 'bna', 'CAN.G1694.2' => 'can', 'CAN.G473.54' => 'can', 'CANSAT01G0816' => 'cansat', 'CANSAT21G1490' => 'cansat', 'CANSAT56G4464' => 'cansat', 'CANSAT64G1259' => 'cansat', 'CANSAT64G1555' => 'cansat', 'CANSAT64G1637' => 'cansat', 'CARHR024640' => 'chi', 'CARHR148650' => 'chi', 'CARHR213790' => 'chi', 'CARHR245800' => 'chi', 'Carub.0001s2376' => 'cru', 'Carub.0005s0563' => 'cru', 'Carub.0007s0288' => 'cru', 'Carub.0007s3476' => 'cru', 'Ca_05076_v3' => 'car', 'Ca_06569_v3' => 'car', 'Ca_06622_v3' => 'car', 'Ca_11723_v3' => 'car', 'Ca_15413_v3' => 'car', 'CBR_g37232' => 'cbr', 'CBR_g51805' => 'cbr', 'CBR_g5666' => 'cbr', 'CBR_g5683' => 'cbr', 'Cc00_g24750' => 'ccan', 'Cc08_g11710' => 'ccan', 'Cc08_g11720' => 'ccan', 'Cc11_g13950' => 'ccan', 'CDE04G1204' => 'cde', 'CDE04G3396' => 'cde', 'CDE05G2199' => 'cde', 'CDE05G3383' => 'cde', 'CDE07G0753' => 'cde', 'CDE07G1758' => 'cde', 'Cfa007285' => 'cfa', 'Cfa007286' => 'cfa', 'Cfa009081' => 'cfa', 'Cfa014098' => 'cfa', 'Ciclev10000715m.g' => 'ccl', 'Ciclev10017544m.g' => 'ccl', 'Ciclev10030976m.g' => 'ccl', 'Ciclev10033880m.g' => 'ccl', 'CiPaw.03G049800' => 'cil', 'CiPaw.04G032700' => 'cil', 'CiPaw.05G144100' => 'cil', 'CiPaw.07G137100' => 'cil', 'ClCG05G013200' => 'cla', 'ClCG05G024890' => 'cla', 'ClCG08G009310' => 'cla', 'ClCG11G006810' => 'cla', 'COL.COLO4_29270' => 'col', 'COL.COLO4_29271' => 'col', 'COL.COLO4_36267' => 'col', 'COL.COLO4_36409' => 'col', 'Cpa.g.sc1097.2' => 'cpa', 'Cpa.g.sc5.316' => 'cpa', 'Cre05.g247500' => 'cre', 'CsaV3_3G027350' => 'csa', 'CsaV3_5G032020' => 'csa', 'CsaV3_6G001280' => 'csa', 'CsaV3_6G031430' => 'csa', 'CSS0004147' => 'camsi', 'CSS0005984' => 'camsi', 'CSS0011940' => 'camsi', 'CSS0013062' => 'camsi', 'CSS0013074' => 'camsi', 'CSS0018087' => 'camsi', 'CSS0025485' => 'camsi', 'CSS0027221' => 'camsi', 'CSS0031107' => 'camsi', 'CSS0044035' => 'camsi', 'DCAR_002963' => 'dca', 'DCAR_013927' => 'dca', 'DCAR_018407' => 'dca', 'DCAR_022970' => 'dca', 'DCAR_024504' => 'dca', 'DCAR_026573' => 'dca', 'Dinv00599' => 'din', 'Dinv24928' => 'din', 'Dinv24929' => 'din', 'Dinv25699' => 'din', 'Dinv31140' => 'din', 'Dinv31141' => 'din', 'Dinv31955' => 'din', 'Dinv33388' => 'din', 'Duzib093G1667' => 'dzi', 'Duzib147G1186' => 'dzi', 'Duzib187G1086' => 'dzi', 'Duzib248G0839' => 'dzi', 'Duzib264G0509' => 'dzi', 'Duzib268G1843' => 'dzi', 'ECA232G2553' => 'eca', 'ECA232G4523' => 'eca', 'ECA238G1906' => 'eca', 'ECA246G4581' => 'eca', 'EL10Ac1g00901' => 'bvu', 'EL10Ac6g13090' => 'bvu', 'EL10Ac6g13445' => 'bvu', 'Eucgr.B03384' => 'egr', 'Eucgr.F03568' => 'egr', 'Eucgr.I01697' => 'egr', 'FAN02G2178' => 'fan', 'FAN04G0289' => 'fan', 'FAN05G3425' => 'fan', 'FAN07G0676' => 'fan', 'FAN09G0292' => 'fan', 'FAN09G0583' => 'fan', 'FAN09G0779' => 'fan', 'FAN09G0866' => 'fan', 'FAN09G1814' => 'fan', 'FAN09G4850' => 'fan', 'FAN12G0036' => 'fan', 'FAN14G2882' => 'fan', 'FAN14G5802' => 'fan', 'FAN17G0702' => 'fan', 'FAN18G0207' => 'fan', 'FAN22G1475' => 'fan', 'FvH4_4g35330' => 'fve', 'FvH4_5g25330' => 'fve', 'FvH4_6g52450' => 'fve', 'FvH4_6g52460' => 'fve', 'FvH4_6g52470' => 'fve', 'Glyma.01G038500' => 'gma', 'Glyma.02G026500' => 'gma', 'Glyma.06G017400' => 'gma', 'Glyma.08G293200' => 'gma', 'Glyma.16G063400' => 'gma', 'Glyma.18G130100' => 'gma', 'Glyma.19G081400' => 'gma', 'Glyma.19G082000' => 'gma', 'Gohir.A01G104600' => 'ghi', 'Gohir.A05G319900' => 'ghi', 'Gohir.A09G032600' => 'ghi', 'Gohir.A09G032700' => 'ghi', 'Gohir.A11G065300' => 'ghi', 'Gohir.D01G089800' => 'ghi', 'Gohir.D05G322200' => 'ghi', 'Gohir.D09G032600' => 'ghi', 'Gohir.D09G032700' => 'ghi', 'Gohir.D11G069600' => 'ghi', 'Gorai.002G115500' => 'gra', 'Gorai.006G037600' => 'gra', 'Gorai.006G037700' => 'gra', 'Gorai.007G074400' => 'gra', 'Gorai.009G345800' => 'gra', 'GSVIVG01003965001' => 'vvi', 'GSVIVG01013379001' => 'vvi', 'GSVIVG01020134001' => 'vvi', 'HanXRQChr05g0144871' => 'han', 'HanXRQChr07g0203371' => 'han', 'HanXRQChr09g0255621' => 'han', 'HanXRQChr14g0451011' => 'han', 'HanXRQChr15g0478261' => 'han', 'Haze_12113' => 'cav', 'Haze_14807' => 'cav', 'Haze_14808' => 'cav', 'Haze_22812' => 'cav', 'Hma1.2p1_0279F.1_g112200' => 'hma', 'Hma1.2p1_0289F.1_g114520' => 'hma', 'Hma1.2p1_0507F.1_g168660' => 'hma', 'HPP92_004596' => 'vpl', 'HPP92_004597' => 'vpl', 'HPP92_011661' => 'vpl', 'HPP92_022689' => 'vpl', 'Hund05936' => 'sun', 'Hund24909' => 'sun', 'Lalb_Chr09g0326591' => 'lal', 'Lalb_Chr11g0061541' => 'lal', 'Lalb_Chr14g0363031' => 'lal', 'Lalb_Chr16g0382611' => 'lal', 'Lalb_Chr23g0265721' => 'lal', 'Lalb_Chr24g0403421' => 'lal', 'Lj1g0007728' => 'lja', 'Lj1g0014156' => 'lja', 'Lj1g0026276' => 'lja', 'Lj2g0005552' => 'lja', 'Lj4P807T8' => 'lonja', 'Lj5E146T0' => 'lonja', 'Lj6g0000499' => 'lja', 'Lj6P798T43' => 'lonja', 'Lj7A605T74' => 'lonja', 'Lj9P297T33' => 'lonja', 'Lju41A46T88' => 'lonja', 'Lju41A46T89' => 'lonja', 'Lju41A46T90' => 'lonja', 'Lsat_1_v5_gn_2_93580' => 'lsa', 'Lsat_1_v5_gn_3_49241' => 'lsa', 'Lsat_1_v5_gn_4_183800' => 'lsa', 'Lsat_1_v5_gn_8_161801' => 'lsa', 'Lsat_1_v5_gn_9_45300' => 'lsa', 'Manes.01G014100' => 'mes', 'Manes.01G049405' => 'mes', 'Manes.01G194200' => 'mes', 'Manes.05G093600' => 'mes', 'Manes.05G123800' => 'mes', 'Manes.15G156000' => 'mes', 'Manes.17G107700' => 'mes', 'Manes.18G004100' => 'mes', 'Manes.S095224' => 'mes', 'Mapoly0001s0534' => 'mpo', 'Mapoly0006s0009' => 'mpo', 'Mapoly0007s0020' => 'mpo', 'Mapoly0077s0009' => 'mpo', 'MBI08_g26555_MAGBIO' => 'mbi', 'MBI11_g32914_MAGBIO' => 'mbi', 'MBI11_g40895_MAGBIO' => 'mbi', 'MD05G1086500' => 'mdo', 'MD06G1009800' => 'mdo', 'MD09G1017800' => 'mdo', 'MD09G1017900' => 'mdo', 'MD16G1083500' => 'mdo', 'MD16G1284700' => 'mdo', 'MD17G1018600' => 'mdo', 'Medtr0044s0160' => 'mtr', 'Medtr1g093975' => 'mtr', 'Medtr1g094005' => 'mtr', 'Medtr2g028920' => 'mtr', 'Medtr3g115540' => 'mtr', 'Medtr5g037020' => 'mtr', 'Medtr7g035445' => 'mtr', 'Medtr7g035455' => 'mtr', 'Medtr7g451350' => 'mtr', 'MELO3C008225.2' => 'cme', 'MELO3C012037.2' => 'cme', 'MELO3C014848.2' => 'cme', 'MELO3C026529.2' => 'cme', 'Migut.E00129' => 'egut', 'Migut.H00053' => 'egut', 'Migut.H00054' => 'egut', 'Migut.L01373' => 'egut', 'Migut.O00321' => 'egut', 'MSTRG.13392' => 'ama', 'MSTRG.2371' => 'ama', 'MSTRG.24062' => 'ama', 'MSTRG.7849' => 'ama', 'Nitab4.5_0000040g0530' => 'nta', 'Nitab4.5_0000407g0100' => 'nta', 'Nitab4.5_0001030g0100' => 'nta', 'Nitab4.5_0001031g0080' => 'nta', 'Nitab4.5_0001031g0120' => 'nta', 'Nitab4.5_0001544g0160' => 'nta', 'Nitab4.5_0001544g0170' => 'nta', 'Nitab4.5_0001863g0200' => 'nta', 'Nitab4.5_0001863g0230' => 'nta', 'Nitab4.5_0004470g0060' => 'nta', 'Nitab4.5_0005414g0040' => 'nta', 'Nitab4.5_0005587g0090' => 'nta', 'Nitab4.5_0006485g0030' => 'nta', 'Nitab4.5_0011499g0010' => 'nta', 'Nn1g01954' => 'nnu', 'Nn3g16573' => 'nnu', 'Nn3g17055' => 'nnu', 'Nn3g19422' => 'nnu', 'Nn4g22453' => 'nnu', 'Nn4g22454' => 'nnu', 'Nn4g22961' => 'nnu', 'Nn4g25625' => 'nnu', 'Nn5g30978' => 'nnu', 'Nn6g31539' => 'nnu', 'Nn6g31712' => 'nnu', 'Oeu000701.1' => 'oeu', 'Oeu015871.1' => 'oeu', 'Oeu026026.1' => 'oeu', 'Oeu030467.1' => 'oeu', 'Oeu034102.1' => 'oeu', 'Oeu044539.2' => 'oeu', 'Oeu048591.1' => 'oeu', 'Oeu050436.1' => 'oeu', 'Oeu058752.1' => 'oeu', 'Os06g0727900' => 'osa', 'Os08g0121900' => 'osa', 'Os12g0267900' => 'osa', 'Peaxi162Scf00064g00123' => 'pax', 'Peaxi162Scf00080g01722' => 'pax', 'Peaxi162Scf00420g00220' => 'pax', 'Peaxi162Scf00420g00254' => 'pax', 'Peaxi162Scf00711g00013' => 'pax', 'Peaxi162Scf00828g10023' => 'pax', 'PGR031G2008' => 'pgr', 'PGR083G2095' => 'pgr', 'PGR102G2564' => 'pgr', 'PGR142G1038' => 'pgr', 'PGSC0003DMG400006969' => 'stu', 'PGSC0003DMG400009987' => 'stu', 'PGSC0003DMG400020230' => 'stu', 'PGSC0003DMG400020271' => 'stu', 'PGSC0003DMG400022633' => 'stu', 'PGSC0003DMG400029403' => 'stu', 'PGSC0003DMG400029404' => 'stu', 'PGSC0003DMG400041816' => 'stu', 'Phvul.002G078300' => 'pvu', 'Phvul.003G072900' => 'pvu', 'Phvul.008G147000' => 'pvu', 'Phvul.008G148200' => 'pvu', 'Phvul.009G011700' => 'pvu', 'Potri.001G336766' => 'ptr', 'Potri.001G336832' => 'ptr', 'Potri.005G252100' => 'ptr', 'Potri.008G192000' => 'ptr', 'Potri.010G039000' => 'ptr', 'Pp3c10_15120' => 'ppa', 'Pp3c1_8510' => 'ppa', 'Pp3c3_25310' => 'ppa', 'Pp3c4_1220' => 'ppa', 'Pp3c4_27110' => 'ppa', 'Pp3c9_11850' => 'ppa', 'Pp3c9_11853' => 'ppa', 'Prupe.1G262500' => 'ppe', 'Prupe.3G299100' => 'ppe', 'Prupe.5G010400' => 'ppe', 'Psat0s1369g0280' => 'psa', 'Psat2g114760' => 'psa', 'Psat3g169040' => 'psa', 'Psat5g010720' => 'psa', 'PSO017G0460' => 'pso', 'PSO063G4178' => 'pso', 'PSO063G5680' => 'pso', 'PSO210G7735' => 'pso', 'PSO339G1540' => 'pso', 'PSO384G2778' => 'pso', 'PSO541G2533' => 'pso', 'PSO591G0450' => 'pso', 'PSO675G0647' => 'pso', 'PSO761G0625' => 'pso', 'PSO832G0304' => 'pso', 'QL02p014605' => 'qlo', 'QL02p073037' => 'qlo', 'QL02p073106' => 'qlo', 'QL02p073163' => 'qlo', 'QL03p067497' => 'qlo', 'RcHm_v2.0_Chr2g0174091' => 'rch', 'RcHm_v2.0_Chr2g0174101' => 'rch', 'RcHm_v2.0_Chr2g0174111' => 'rch', 'RcHm_v2.0_Chr4g0444941' => 'rch', 'RcHm_v2.0_Chr7g0215561' => 'rch', 'Rhsim06G0006200' => 'rsi', 'Rhsim07G0256600' => 'rsi', 'Rhsim10G0011600' => 'rsi', 'Rhsim10G0011700' => 'rsi', 'Rhsim10G0011800' => 'rsi', 'Rhsim12G0052400' => 'rsi', 'Sabra05G0195500' => 'sbr', 'Sabra08G0145500' => 'sbr', 'Sabra10G0027400' => 'sbr', 'Sabra16G0217600' => 'sbr', 'Sabra16G0217700' => 'sbr', 'SalBow7G2506' => 'sbo', 'SalBow7G2910' => 'sbo', 'Sc03g0006890' => 'sci', 'Sc03g0007010' => 'sci', 'Sc11g0001500' => 'sci', 'Sc14g0008510' => 'sci', 'Sc16g0003720' => 'sci', 'Sed0000420' => 'sed', 'Sed0005287' => 'sed', 'Sed0014177' => 'sed', 'Sed0017932' => 'sed', 'Sed0019906' => 'sed', 'Sed0025932' => 'sed', 'SEGI_00116' => 'sgi', 'SEGI_13207' => 'sgi', 'SEGI_15562' => 'sgi', 'SEGI_18332' => 'sgi', 'SEGI_37371' => 'sgi', 'SEGI_40457' => 'sgi', 'SGA_v2.0_scaffold135G34937' => 'sas', 'SGA_v2.0_scaffold166G38307' => 'sas', 'SGA_v2.0_scaffold319G48550' => 'sas', 'SGA_v2.0_scaffold47G17542' => 'sas', 'SGA_v2.0_scaffold87G26990' => 'sas', 'SHI03853' => 'shi', 'SHI20713' => 'shi', 'SMO141G0125' => 'smo', 'SMO141G0128' => 'smo', 'Solyc02g067970.4' => 'sly', 'Solyc02g093750.3' => 'sly', 'Solyc02g093760.4' => 'sly', 'Solyc04g082520.3' => 'sly', 'Solyc05g006560.1' => 'sly', 'Solyc12g094670.1' => 'sly', 'Sopen02g017100' => 'spe', 'Sopen02g038390' => 'spe', 'Sopen02g038400' => 'spe', 'Sopen04g036140' => 'spe', 'Sopen05g002510' => 'spe', 'Sopen12g031570' => 'spe', 'Sp1g21570' => 'spa', 'Sp2g16520' => 'spa', 'Sp7g35080' => 'spa', 'TAR371G0949' => 'tar', 'TAR371G1081' => 'tar', 'TAR374G1481' => 'tar', 'TAR376G0130' => 'tar', 'TAR381G0649' => 'tar', 'TAR446G0002' => 'tar', 'TAR622G0035' => 'tar', 'TAR628G0757' => 'tar', 'TAR629G0251' => 'tar', 'TAR629G0841' => 'tar', 'THA.LOC104801955' => 'tha', 'THA.LOC104805349' => 'tha', 'THA.LOC104822073' => 'tha', 'THA.LOC104822944' => 'tha', 'THA.LOC104823964' => 'tha', 'THA.LOC104825305' => 'tha', 'Thecc.02G238200' => 'tca', 'Thecc.04G025000' => 'tca', 'Thecc.04G025100' => 'tca', 'Thecc.04G027000' => 'tca', 'Thecc.08G060900' => 'tca', 'Thhalv10003629m.g' => 'esa', 'Thhalv10007185m.g' => 'esa', 'Thhalv10027280m.g' => 'esa', 'Thhalv10028205m.g' => 'esa', 'TPR.G26705' => 'tpr', 'TPR.G3617' => 'tpr', 'TPR.G38200' => 'tpr', 'TPR.G9071' => 'tpr', 'TPR.G9072' => 'tpr', 'TWI12G0650' => 'twi', 'TWI36G1264' => 'twi', 'TWI36G1408' => 'twi', 'TWI56G1312' => 'twi', 'TWI75G1660' => 'twi', 'unitig_21.g20485' => 'ugi', 'unitig_22.g6486' => 'ugi', 'vmacro04414' => 'vma', 'vmacro05918' => 'vma', 'vmacro05919' => 'vma', 'vmacro16035' => 'vma', 'VMungo0251G2894' => 'vmu', 'VMungo0720G0730' => 'vmu', 'VMungo1215G1136' => 'vmu', 'VMungo1309G1887' => 'vmu', 'Zm00001eb111820' => 'zma', 'Zm00001eb173440' => 'zma', 'Zm00001eb271980' => 'zma', 'Zm00001eb331370' => 'zma' ) $gf_id = 'HOM05D001177' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001177' ) $data_identifier = 'HOM05D001177' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 6, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 9, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 14, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 8, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 6, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb331370' $species_info = array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) $local_species = 'zma' $disabled = '' $selected = '' $num_hits = (int) 1